Introduction to guidelines
Services and fees
The mission of the PAF of the University of Lausanne is to support the local research community in the analysis of proteins and proteomes. To help support its activity and equipment purchases, the facility operates with fees, which apply to a well defined list of analyses. Such fees are differentiated depending of the affiliation of the user(s) and are presented in the catalog of the PAF official services (http://www.unil.ch/paf/page12982_en.html ).
The PAF does not have dedicated funding for carrying out collaborative projects. Therefore, in principle all PAF users have to arrange payment of their analyses according to the fees and categories mentioned above. Exceptions are listed below.
We strongly encourage investigators to request specific funding for proteomics at the time of grant application. The facility coordinator can provide support and suggestions for the writing of research proposals and can of course prepare letters of support and confirmation.
For manuscript writing, the PAF will provide the users upon request i) descriptions of materials and methods relevant to the experiments performed ii) comprehensive supplementary tables in a format accepted by most journals (.txt, .pdf or .xls) and iii) all the raw data if required. Unless agreed differently (see below) the PAF will not prepare publication-style tables and figures to be included in the main article body nor write portions of article text.
As a minimum, the work carried out by the PAF should be acknowledged in all publications which either present data directly produced by the facility or results for the generation of which the work of the PAF played an important role. The name and affiliation of the facility should be fully and correctly mentioned as follows :
“Protein Analysis Facility, Center for Integrative Genomics, Faculty of Biology and Medecine, University of Lausanne, Switzerland”.
No specific person names need to be listed, unless desired by the authors.
In general we apply the guidelines established by the International Committee of Medical Journal Editors and similar organizations as discussed by Huth (Huth, E. J.  Guidelines on Authorship of Medical Papers, Annals Int. Med. 104 : 269-274) and Bailey (Bailey, B. J.  What Is an Author? Otolaryngol. Head Neck Surg. 124 :2-3 ).
These guidelines suggest that if scientists from the PAF have significantly helped to design or conceive the experiments, have done non-standard analysis and interpretation of data, or both, they should be coauthors of papers that use data generated by the facility. In this case facility scientists should participate in drafting the paper or revising it for critically important content, and give final approval of the version to be published. If these conditions are not met, the PAF should appear only in the acknowledgements (see above). In case of uncertainty about authorship, the investigator should clarify these issues with the facility coordinator, preferably before start of the experiments.
We define two types of collaborations :
1) User-initiated collaborations are those in which the proponent is a PAF user ( usually a biomedical researcher). The PAF coordinator, in agreement with his Steering Committee, can accept to carry out such collaborative projects in which the PAF makes its technological platform available to push the limits of analysis on a set of relevant and challenging samples. Such projects are in principle subject to the same fees as routine work. The proponent should provide a written statement in advance on the availability of sufficient funding. In such projects, the personnel of the PAF engages in a closer collaboration with the user group to provide optimized support and improve aspects such as experimental design, sample preparation and data analysis. Also, the PAF team can decide to use the samples from the project to implement and test new technologies which are not yet part of the regular catalog of services. In such case, these analyses can (but must not be) be free of charge. For this type of collaborations, the PAF members involved will be co-authors of resulting publications. The details of co-authorship (position, etc) should be discussed at the beginning of the project.
2) PAF-initiated collaborations : the PAF can contact biomedical investigators to propose collaborations. One of the primary purposes is to acquire challenging biological samples for the implementation, test or development of new techniques which are not yet in the regular catalog of PAF services. Such analyses are generally free of charge for the user. The PAF coordinator has to ensure, in planning such experiments, that i) the workload is compatible with the capacity of the platform, ii) that it does not interfere with the normal operation of the PAF service and iii) that it does not lead to a significant increase in the waiting times for other regular users. For this type of collaborations the PAF members involved will be co-authoring the resulting publications together with the lab providing the samples. The details of co-authorship should be discussed at the beginning of the project.